obtain_mod_Comet {PepMapViz} | R Documentation |
Obtain modification information from Peptide data generated by Comet
Description
This function takes Comet output containing a column with modified peptide sequences including PTM information and converts it into a new dataframe with the desired format of peptide sequences and associated PTM information.
Usage
obtain_mod_Comet(
data,
mod_column,
PTM_table = NULL,
PTM_annotation = FALSE,
PTM_mass_column
)
Arguments
data |
A data.table with a column containing PTM information. |
mod_column |
The name of the column containing the modified peptide sequences. |
PTM_table |
A data.table with columns 'PTM_mass' and 'PTM_type' containing PTM annotation information. |
PTM_annotation |
A logical value indicating whether to include PTM annotation information in the result. |
PTM_mass_column |
The name of the column containing the PTM mass information |
Value
A data.table with 'PTM_position', 'PTM_type', 'reps', and other columns.
Examples
library(data.table)
data <- data.table(
modified_peptide = c(
"AAM[15.9949]Q[-0.98]RGSLYQCDYSTGSC[57.02]EPIR",
"K.AAQQTGKLVHANFGT.K",
"K.[-0.98]AATVTGKLVHANFGT.K"
),
plain_peptide = c(
"AAMQRGSLYQCDYSTGSCEPIR",
"AAQQTGKLVHANFGT",
"AATVTGKLVHANFGT"
),
Condition = c("A", "B", "B")
)
PTM_table <- data.table(
PTM_mass = c(57.02, -0.98, 15.9949),
PTM_type = c("Cam", "Amid", "Ox")
)
mod_column <- 'modified_peptide'
PTM_mass_column <- "PTM_mass"
converted_data <- obtain_mod_Comet(data, mod_column, PTM_table,
PTM_annotation = TRUE, PTM_mass_column)
[Package PepMapViz version 1.1.0 Index]